Corrigendum to "Phylogenomic re-assessment of the thermophilic genus Geobacillus" [Syst. Appl. Microbiol. 39 (2016) 527-533].

Syst Appl Microbiol. 2018 Jul 10;:

Authors: Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P

PMID: 30006234 [PubMed - as supplied by publisher]

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

BMC Genomics. 2018 Jul 13;19(1):536

Authors: Xue Z, Warren RL, Gibb EA, MacMillan D, Wong J, Chiu R, Hammond SA, Yang C, Nip KM, Ennis CA, Hahn A, Reynolds S, Birol I

Abstract
BACKGROUND: Alternative polyadenylation (APA) results in messenger RNA molecules with different 3' untranslated regions (3' UTRs), affecting the molecules' stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3' UTR length modifications and commonly characterized APA events as 3' UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3' ends of transcripts and fails to adequately describe the various scenarios we observe.
RESULTS: We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT. We applied this pipeline to elucidate the APA profiles of 114 genes in 9939 tumor and 729 tissue normal samples from The Cancer Genome Atlas (TCGA). The full set of 10,668 RNA-Seq samples from 33 cancer types has not been utilized by previous APA studies. By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types; for 15 genes, such regulation is recurrent across multiple cancers. Our results also support a previous report showing the 3' UTR shortening of FGF2 in multiple cancers. However, over half of the events we identified display complex changes to 3' UTR length that resist simple classification like shortening or lengthening.
CONCLUSIONS: Recurrent tumor-specific regulation of APA is widespread in cancer. However, the regulation pattern that we observed in TCGA RNA-seq data cannot be described as straightforward 3' UTR shortening or lengthening. Continued investigation into this complex, nuanced regulatory landscape will provide further insight into its role in tumor formation and development.

PMID: 30005633 [PubMed - in process]

32 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/14

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26 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/14

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20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/13

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15 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/13

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

19 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

18 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

48 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/11

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42 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/10

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Proteome profiling in the hippocampus, medial prefrontal cortex, and striatum of aging rat.

Exp Gerontol. 2018 Jul 04;:

Authors: Hamezah HS, Durani LW, Yanagisawa D, Ibrahim NF, Aizat WM, Bellier JP, Makpol S, Ngah WZW, Damanhuri HA, Tooyama I

Abstract
Decrease in multiple functions occurs in the brain with aging, all of which can contribute to age-related cognitive and locomotor impairments. Brain atrophy specifically in hippocampus, medial prefrontal cortex (mPFC), and striatum, can contribute to this age-associated decline in function. Our recent metabolomics analysis showed age-related changes in these brain regions. To further understand the aging processes, analysis using a proteomics approach was carried out. This study was conducted to identify proteome profiles in the hippocampus, mPFC, and striatum of 14-, 18-, 23-, and 27-month-old rats. Proteomics analysis using ultrahigh performance liquid chromatography coupled with Q Exactive HF Orbitrap mass spectrometry identified 1074 proteins in the hippocampus, 871 proteins in the mPFC, and 241 proteins in the striatum. Of these proteins, 97 in the hippocampus, 25 in mPFC, and 5 in striatum were differentially expressed with age. The altered proteins were classified into three ontologies (cellular component, molecular function, and biological process) containing 44, 38, and 35 functional groups in the hippocampus, mPFC, and striatum, respectively. Most of these altered proteins participate in oxidative phosphorylation (e.g. cytochrome c oxidase and ATP synthase), glutathione metabolism (e.g. peroxiredoxins), or calcium signaling pathway (e.g. protein S100B and calmodulin). The most prominent changes were observed in the oldest animals. These results suggest that alterations in oxidative phosphorylation, glutathione metabolism, and calcium signaling pathway are involved in cognitive and locomotor impairments in aging.

PMID: 29981398 [PubMed - as supplied by publisher]

Validation of the binary designation 'Symbiodinium thermophilum' (Dinophyceae).

J Phycol. 2018 Jul 07;:

Authors: Hume BCC, D'Angelo C, Smith EG, Stevens JR, Burt JA, Wiedenmann J

Abstract
The binary designation 'Symbiodinium thermophilum' was invalid due to the absence of an illustration as required by Article 44.2 of the ICN. Herein, it is validated. This species is the most common symbiont in reef corals in the southern Persian/Arabian Gulf (PAG), the world's hottest body of water sustaining reef coral growth. This article is protected by copyright. All rights reserved.

PMID: 29981276 [PubMed - as supplied by publisher]

A Critical Comparison of Rejection-Based Algorithms for Simulation of Large Biochemical Reaction Networks.

Bull Math Biol. 2018 Jul 06;:

Authors: Thanh VH

Abstract
The rejection-based simulation technique has been applying to improve the computational efficiency of the stochastic simulation algorithm (SSA) in simulating large reaction networks, which are required for a thorough understanding of biological systems. We compare two recently proposed simulation methods, namely the composition-rejection algorithm (SSA-CR) and the rejection-based SSA (RSSA), aiming for this purpose. We discuss the right interpretation of the rejection-based technique used in these algorithms in order to make an informed choice when dealing with different aspects of biochemical networks. We provide the theoretical analysis as well as the detailed runtime comparison of these algorithms on concrete biological models. We highlight important factors that are omitted in previous analysis of these algorithms. The numerical comparison shows that for reaction networks where the search cost is expensive then SSA-CR is more efficient, and for reaction networks where the update cost is dominant, often the case in practice, then RSSA should be the choice.

PMID: 29981002 [PubMed - as supplied by publisher]

Advanced tools for the safety assessment of nanomaterials.

Nat Nanotechnol. 2018 Jul;13(7):537-543

Authors: Fadeel B, Farcal L, Hardy B, Vázquez-Campos S, Hristozov D, Marcomini A, Lynch I, Valsami-Jones E, Alenius H, Savolainen K

Abstract
Engineered nanomaterials (ENMs) have tremendous potential to produce beneficial technological impact in numerous sectors in society. Safety assessment is, of course, of paramount importance. However, the myriad variations of ENM properties makes the identification of specific features driving toxicity challenging. At the same time, reducing animal tests by introducing alternative and/or predictive in vitro and in silico methods has become a priority. It is important to embrace these new advances in the safety assessment of ENMs. Indeed, remarkable progress has been made in recent years with respect to mechanism-based hazard assessment of ENMs, including systems biology approaches as well as high-throughput screening platforms, and new tools are also emerging in risk assessment and risk management for humans and the environment across the whole life-cycle of nano-enabled products. Here, we highlight some of the key advances in the hazard and risk assessment of ENMs.

PMID: 29980781 [PubMed - in process]

Imaging the Vascular Bone Marrow Niche During Inflammatory Stress.

Circ Res. 2018 Jul 06;:

Authors: Vandoorne K, Rohde D, Kim HY, Courties G, Wojtkiewicz GR, Honold L, Hoyer FF, Frodermann V, Nayar R, Herisson FE, Jung Y, Désogère P, Vinegoni C, Caravan P, Weissleder R, Sosnovik DE, Lin CP, Swirski FK, Nahrendorf M

Abstract
Rationale: Inflammatory stress induced by exposure to bacterial lipopolysaccharide (LPS) causes hematopoietic stem cell (HSC) expansion in the bone marrow niche, generating a cellular immune response. As an integral component of the hematopoietic stem cell niche, the bone marrow vasculature regulates the production and release of blood leukocytes, which protect the host against infection but also fuel inflammatory diseases. Objective: We aimed to develop imaging tools to explore vascular changes in the bone marrow niche during acute inflammation. Methods and Results: Using the Toll-like receptor ligand LPS as a prototypical danger signal, we applied multi-parametric, -modality and -scale imaging to characterize how the bone marrow vasculature adapts when hematopoiesis boosts leukocyte supply. In response to LPS, ex vivo flow cytometry and histology showed vascular changes to the bone marrow niche. Specifically, proliferating endothelial cells gave rise to new vasculature in the bone marrow during hypoxic conditions. We studied these vascular changes with complementary intravital microscopy and PET/MR imaging. Fluorescence and PET integrin αVβ3 imaging signal increased during LPS-induced vascular remodeling. Vascular leakiness, quantified by albumin-based in vivo microcopy and MRI, rose when neutrophils departed and hematopoietic stem and progenitor cells (HSPC) proliferated more vigorously. Conclusions: Introducing a tool set to image bone marrow either with cellular resolution or non-invasively within the entire skeleton, this work sheds light on angiogenic responses that accompany emergency hematopoiesis. Understanding and monitoring bone marrow vasculature may provide a key to unlock therapeutic targets regulating systemic inflammation.

PMID: 29980569 [PubMed - as supplied by publisher]

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/07

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/07

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

28 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/06

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

28 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2018/07/06

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Multiple inputs ensure yeast cell size homeostasis during cell cycle progression.

Elife. 2018 Jul 04;7:

Authors: Garmendia-Torres C, Tassy O, Matifas A, Molina N, Charvin G

Abstract
Coordination of cell growth with division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established remains to be discovered. Here, we developed a new technique based on quantification of histone levels to monitor cell cycle progression in individual cells with unprecedented accuracy. Our analysis establishes the existence of a mechanism controlling bud size in G2/M that prevents premature onset of anaphase, and controls the overall size variability. While most G1 mutants do not display impaired size homeostasis, mutants in which Cyclin B-Cdk regulation is altered display large size variability. Our study thus demonstrates that size homeostasis is not controlled by a G1-specific mechanism alone but is likely to be an emergent property resulting from the integration of several mechanisms that coordinate cell and bud growth with division.

PMID: 29972352 [PubMed - as supplied by publisher]